4Y90

Crystal structure of Triosephosphate Isomerase from Deinococcus radiodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins.

Romero-Romero, S.Costas, M.Rodriguez-Romero, A.Alejandro Fernandez-Velasco, D.

(2015) Phys Chem Chem Phys 17: 20699-20714

  • DOI: 10.1039/c5cp01599e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Temperature is one of the main variables that modulate protein function and stability. Thermodynamic studies of oligomeric proteins, the dominant protein natural form, have been often hampered because irreversible aggregation and/or slow reactions ar ...

    Temperature is one of the main variables that modulate protein function and stability. Thermodynamic studies of oligomeric proteins, the dominant protein natural form, have been often hampered because irreversible aggregation and/or slow reactions are common. There are no reports on the reversible equilibrium thermal unfolding of proteins composed of (β/α)8 barrel subunits, albeit this "TIM barrel" topology is one of the most abundant and versatile in nature. We studied the eponymous TIM barrel, triosephosphate isomerase (TIM), belonging to five species of different bacterial taxa. All of them were found to be catalytically efficient dimers. The three-dimensional structure of four enzymes was solved at high/medium resolution. Irreversibility and kinetic control were observed in the thermal unfolding of two TIMs, while for the other three the thermal unfolding was found to follow a two-state equilibrium reversible process. Shifts in the global stability curves of these three proteins are related to the organismal temperature range of optimal growth and modulated by variations in maximum stability temperature and in the enthalpy change at that temperature. Reversibility appears to correlate with the low isoelectric point, the absence of a residual structure in the unfolded state, small cavity volume in the native state, low conformational stability and a low melting temperature. Furthermore, the strong coupling between dimer dissociation and monomer unfolding may reduce aggregation and favour reversibility. It is therefore very thought-provoking to find that a common topological ensemble, such as the TIM barrel, can unfold/refold in the Anfinsen way, i.e. without the help of the cellular machinery.


    Organizational Affiliation

    Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Distrito Federal, Mexico. fdaniel@unam.mx.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Triosephosphate isomerase
A, B, C, D
247Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Mutation(s): 0 
Gene Names: tpiA
EC: 5.3.1.1
Find proteins for Q9RUP5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RUP5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.136 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 169.620α = 90.00
b = 169.620β = 90.00
c = 202.266γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
CrystalCleardata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia de MexicoMexico166472
Consejo Nacional de Ciencia y Tecnologia de MexicoMexico99857

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Data collection
  • Version 1.2: 2015-08-12
    Type: Database references
  • Version 1.3: 2017-11-01
    Type: Author supporting evidence, Derived calculations